Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Value Type Interaction Map description Network Comparison Type Rank Gene red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 932 to 981 of 3228 in total 
Value Type	Measured
Interaction Map	High confidence
Network Comparison Type	Divided
Filtered	1

description	Rank	red	green	network_comparison	
endosome-associated fyve-domain protein. [source:refseq;acc:nm_014733]	3200	0.00001	0.00001	1	
endothelial-derived gene 1. [source:refseq;acc:nm_025205]	1807	6399.54	6818.17	1.06542	
enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [source:swissprot;acc:q14511]	202	4812.01	6076.09	1.26269	
enhancer of rudimentary homolog. [source:swissprot;acc:q14259]	2072	6437.24	6797.24	1.05592	
enhancer of zeste homolog 1 (enx-2). [source:swissprot;acc:q92800]	3090	0.00001	0.00001	1	
enhancer of zeste homolog 2 (enx-1). [source:swissprot;acc:q15910]	3098	0.00001	0.00001	1	
enigma protein; lim domain protein. [source:refseq;acc:nm_005451]	1596	5665.34	6070.32	1.07148	
enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [source:swissprot;acc:p30084]	504	10067.9	11511	1.14334	
enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [source:swissprot;acc:p98073]	347	4991.02	5885.09	1.17914	
enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [source:refseq;acc:nm_014666]	2022	5520.26	5841.16	1.05813	
epidermal growth factor receptor kinase substrate eps8. [source:swissprot;acc:q12929]	1261	5685.34	6157.53	1.08305	
epidermal growth factor receptor pathway substrate 8-like protein 1 isoform c; epidermal growth factor receptor pathway substrate 8-related protein 1; eps8-related protein 1. [source:refseq;acc:nm_139204]	1259	5685.38	6157.7	1.08308	
epidermal growth factor receptor pathway substrate 8-like protein 2; eps8-related protein 2; epidermal growth factor receptor pathway substrate 8-related protein 2. [source:refseq;acc:nm_022772]	1270	5685.08	6156.48	1.08292	
epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [source:swissprot;acc:p00533]	1391	5743.36	6192.7	1.07824	
epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [source:swissprot;acc:q15668]	872	6781.05	7480.15	1.1031	
epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [source:swissprot;acc:p12830]	2173	3641.4	3462.96	1.05153	
epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [source:swissprot;acc:p07099]	1573	11785.4	10995.3	1.07186	
epsin 1; eh domain-binding mitotic phosphoprotein. [source:refseq;acc:nm_013333]	1801	5881.33	6268.57	1.06584	
epsin 2 isoform b; eps15 binding protein. [source:refseq;acc:nm_014964]	1794	5948.26	6342.84	1.06634	
epsin 3. [source:refseq;acc:nm_017957]	1809	5816.12	6196.21	1.06535	
ergic-53 protein precursor (er-golgi intermediate compartment 53 kda protein) (lectin, mannose-binding 1) (gp58) (intracellular mannose specific lectin mr60). [source:swissprot;acc:p49257]	3177	0.00001	0.00001	1	
ero1-like. [source:refseq;acc:nm_014584]	855	6562.98	7242.37	1.10352	
erythroid differentiation and denucleation factor 1. [source:swissprot;acc:o60584]	2128	5328.73	5616.59	1.05402	
erythroid differentiation-related factor 1. [source:refseq;acc:nm_015608]	3095	0.00001	0.00001	1	
espin. [source:refseq;acc:nm_031475]	1876	6076.66	6463.12	1.0636	
esterase d (ec 3.1.1.1). [source:swissprot;acc:p10768]	2250	6834.03	7153.66	1.04677	
estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [source:swissprot;acc:p14061]	2520	5964.17	6113.96	1.02511	
estradiol 17 beta-dehydrogenase 4 (ec 1.1.1.62) (17-beta-hsd 4) (17-beta-hydroxysteroid dehydrogenase 4). [source:swissprot;acc:p51659]	2538	7121.07	7286.61	1.02325	
estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [source:swissprot;acc:o75454]	902	10246.1	11285.8	1.10147	
ethanolamine kinase (ec 2.7.1.82) (eki). [source:swissprot;acc:q9hbu6]	2328	6773.67	7075.51	1.04456	
ethanolamine kinase-like protein eki2 (flj10761). [source:swissprot;acc:q9nvf9]	2327	6773.67	7075.51	1.04456	
ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [source:swissprot;acc:q99447]	749	4565.34	5085.92	1.11403	
eukaryotic initiation factor 4a-i (eif-4a-i) (eif4a-i). [source:swissprot;acc:p04765]	2868	0.00001	0.00001	1	
eukaryotic initiation factor 4a-ii (eif-4a-ii) (eif4a-ii). [source:swissprot;acc:q14240]	2888	0.00001	0.00001	1	
eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [source:swissprot;acc:p46055]	2621	5599.85	5683	1.01485	
eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [source:swissprot;acc:p05198]	2031	5060.82	5350.93	1.05732	
eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [source:swissprot;acc:p20042]	1753	5423.67	5787.46	1.06707	
eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [source:swissprot;acc:p41091]	1882	5490.24	5838.67	1.06346	
eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [source:swissprot;acc:q14152]	743	4131.04	4607.9	1.11543	
eukaryotic translation initiation factor 3 subunit 11 (eif-3 p25) (eif3k) (muscle specific gene m9 protein) (ptd001) (hspc029) (arg134). [source:swissprot;acc:q9ubq5]	2127	5328.73	5616.59	1.05402	
eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [source:swissprot;acc:q13347]	612	3975.77	4485.05	1.1281	
eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [source:swissprot;acc:o75821]	742	4131.04	4607.9	1.11543	
eukaryotic translation initiation factor 3 subunit 6 interacting protein (hspc021/hspc025). [source:swissprot;acc:q9y262]	2133	5328.73	5616.59	1.05402	
eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [source:swissprot;acc:o15371]	1597	5665.34	6070.32	1.07148	
eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [source:swissprot;acc:q99613]	923	4057.54	4457.66	1.09861	
eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [source:swissprot;acc:p55884]	684	4359.82	4880.99	1.11954	
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [source:swissprot;acc:q04637]	186	4071.1	5251.75	1.29001	
eukaryotic translation initiation factor 4 gamma, 3. [source:refseq;acc:nm_003760]	181	4068.56	5252.6	1.29102	
eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [source:swissprot;acc:p06730]	393	4490.28	5222.25	1.16301	
eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	273	3199.4	3870.8	1.20985	

Legend:
- Rank is the rank after comparing the two networks
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/